Estimating the location and shape of hybrid zones

We propose a new model to make use of georeferenced genetic data for inferring the location and shape of a hybrid zone. The model output includes the posterior distribution of a parameter that quantifies the width of the hybrid zone. The model proposed is implemented in the GUI and command-line versions of the Geneland program versions ≥ 3.3.0. Information about the program can be found on http://www2.imm.dtu.dk/gigu/Geneland/.     

Site-directed mutagenesis of Escherichia coli 23 S ribosomal RNA at position 1067 within the GTP hydrolysis centre

Site-directed mutagenesis has been used to change, specifically, residue 1067 within 23 S ribosomal RNA of Escherichia coli. This nucleoside (adenosine in the wild-type sequence) lies within the GTPase centre of the larger ribosomal subunit and is normally the target for the methylase enzyme responsible for resistance to the antibiotic thiostrepton. The performance of the altered ribosomes was not impaired in cell-free protein synthesis nor in GTP hydrolysis assays (although the 3 mutant strains grew somewhat more slowly than wild-type) but their responses to thiostrepton did vary. Thus, ribosomes containing the A to C or A to U substitution at residue 1067 of 23 S rRNA were highly resistant to the drug, whereas the A to G substitution resulted in much lesser impairment of thiostrepton binding and the ribosomes remained substantially sensitive to the antibiotic. These data reinforce the hypothesis that thiostrepton binds to 23 S rRNA at a site that includes residue A1067. They also exclude any possibility that the insensitivity of eukaryotic ribosomes to the drug might be due solely to the substitution of G at the equivalent position within eukaryotic rRNA.     

Acoustic communication in a king penguin colony: importance of bird location within the colony and of the body position of the listener

This study focuses on the propagation of the display call used for individual recognition between penguin partners. Transmission of acoustic information in a noisy environment such as a king penguin colony is very difficult. Conditions of propagation were examined for two areas of the colony (hatching and courtship areas) and reception at three heights from the ground (10, 45 and 90 cm). Signal modification was assessed in terms of attenuation of signal, amplitude modulation and spectral content. The acoustic recognition of the mate, which is decisive for breeding success, took place in the hatching area where signal degradation was less great for all parameters studied. When the receiver was located 10 cm above the ground, degradation of the signal was much more pronounced than when it was located 45 or 90 cm above ground. The characteristic incubating attitude of the king penguin (i.e. standing with the head at 45 cm above the ground) enables it to receive the main part of the signal in spite of the noisy environment. Accepted: 19 October 1998     

Spatial compatibility and position of the effectors

Mean reaction times obtained with crossed hands (right had on the left and left hand on the right) are slower than reaction times obtained with uncrossed hands (right hand on the right and left hand on the left). These results have been explained as a compatibility effect between the responding hand and its spatial position. The goal of the present experiment was to establish whether the position of the hand is encoded by the subjects relative to their body (absolute position) or relative to the other hand (relative position). The subjects performed a discrimination task on two visual stimuli. Stimuli and hands were either on the same side of the body (both on the left or both on the right) or had different absolute position. In all conditions the subjects responded with crossed and uncrossed hands. The results support the hypothesis that relative position is encoded.     

Small cytoplasmic RNAs and their location within the cytoplasm

These studies were designed to establish the location of various species of small RNAs within the subcellular cytoplasmic compartments. Four cytoplasmic RNA-containing compartments were examined: (A) cytoskeleton-bound polyribosomal ribonucleoprotein (RNP) complexes, (B) soluble-phase polyribosomal RNP complexes, (C) cytoskeleton-bound free RNP complexes, (D) soluble-phase free RNP complexes. The presence of the small cytoplasmic RNA (scRNA) population and histone H4 and actin mRNAs in each compartment was examined to determine their spatial distribution within the cytoplasm. The 7S signal recognition RNA and the 5S and 5.8S rRNAs were distributed among all four compartments, while 4S tRNAs were localized largely in fraction D. Fraction C contained a group of seven abundant scRNAs, of approximately 105-348 nucleotides in length, which were localized almost entirely within the cytoskeleton-bound free RNP compartment. Actin mRNAs were localized in fraction A, the actively translating cytoskeleton-bound compartment. Actin mRNAs were localized in fraction A, the actively translating cytoskeleton-bound compartment. Following cytochalasin B treatment, actin mRNAs were released into the soluble phase, implicating a dependence on the integrity of actin filaments in its binding. Such treatment also released several of the scRNAs from their cytoskeleton-bound location. In contrast histone H4 mRNAs were much more widely dispersed, being present in all four cytoskeletal compartments. Approximately 60% of the H4 mRNAs, however, were localized within the soluble-phase polyribosomes in fraction B. Cytochalasin B treatment released only the small portion of untranslated histone H4 mRNA associated with the cytoskeleton in fraction C, suggesting that the binding of these H4 mRNAs was dependent in some manner upon the integrity of actin filaments.     

Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank

Despite its immense size, logistical and methodological constraints have largely limited microbiological investigations of the subseafloor basement biosphere. In this study, a unique sampling system was used to collect fluids from the subseafloor basaltic crust via a Circulation Obviation Retrofit Kit (CORK) observatory at Integrated Ocean Drilling Program borehole 1301A, located at a depth of 2667 m in the Pacific Ocean on the eastern flank of the Juan de Fuca Ridge. Here, a fluid delivery line directly accesses a 3.5 million years old basalt-hosted basement aquifer, overlaid by 262 m of sediment, which serves as a barrier to direct exchange with bottom seawater. At an average of 1.2 × 10⁴ cells ml⁻¹, microorganisms in borehole fluids were nearly an order of magnitude less abundant than in surrounding bottom seawater. Ribosomal RNA genes were characterized from basement fluids, providing the first snapshots of microbial community structure using a high-integrity fluid delivery line. Interestingly, microbial communities retrieved from different CORKs (1026B and 1301A) nearly a decade apart shared major community members, consistent with hydrogeological connectivity. However, over three sampling years, the dominant gene clone lineage changed from relatives of Candidatus Desulforudis audaxviator within the bacterial phylum Firmicutes in 2008 to the Miscellaneous Crenarchaeotic Group in 2009 and a lineage within the JTB35 group of Gammaproteobacteria in 2010, and statistically significant variation in microbial community structure was observed. The enumeration of different phylogenetic groups of cells within borehole 1301A fluids supported our observation that the deep subsurface microbial community was temporally dynamic.     

Spatial variation in demography and population growth rate: the importance of natal location

1. Understanding the pattern and magnitude of spatial variation in demography and population growth rate (lambda) is key to understanding the structure and dynamics of natural populations. However, such spatial variation is challenging to quantify. We use>20 years of individual life-history data to quantify small- and large-scale spatial variation in demography and lambda within a single population of red-billed choughs Pyrrhocorax pyrrhocorax on Islay, Scotland. Critically, we demonstrate a major importance of an individual's natal rather than current location in driving observed spatial variation. 2. Breeding success (the number of offspring fledged per breeding attempt) varied among individual chough nest sites but did not vary on a larger spatial scale across Islay. 3. The proportion of fledglings observed to survive to recruiting age varied markedly among individual nest sites and also varied more widely across Islay. Spatial capture-mark-recapture models defined two discrete geographical regions where fledgling survival differed significantly: choughs fledged in region 'BGE' were more likely to survive than choughs fledged in region 'CNSW' as both subadults and adults. 4. The asymptotic lambda attributable to breeding attempts in region BGE exceeded unity, and exceeded that attributable to breeding attempts in region CNSW. Relatively productive and unproductive regions therefore exist within this population. 5. Spatial variation in adult survival was better explained by an individual's natal region than the region where that individual settled to breed. Spatial variation in lambda would consequently have remained undetected had survival been measured across resident breeders rather than across individuals fledged in each region. Furthermore, breeding success was a weak predictor of a nest site's estimated productivity of recruits. 6. We therefore describe marked spatial variation in demography and lambda within a single population of a territorial vertebrate, mediated partly by long-term links between an individual's natal location and its subsequent life-history. Life-long monitoring of individuals of known origin may therefore be necessary to identify accurately subpopulations of intrinsically high and low lambda.     

Dynamics of chromatin position within the interphase nucleus

In this article we attempt to analyze the relationship between the processes, which occur in the nucleus, and the dynamics of chromatin, as well as to classify the changes in the position of chromatin in the cell nucleus during the lifetime of the cell. The proposed concept integrates possible types of chromatin movement within the nucleus.     

The effect of centre of mass location on sagittal plane moments around the centre of mass in trotting horses

The diagonal limb support pattern at trot provides pitch and roll stability, but little is known about the control of moments about the centre of mass (COM) in horses. Correct COM location is critical in the calculation of pitching moments. The objectives were to determine the effect of COM location on pitching moments in trotting horses and explore how COM location could influence balance.     

The phylogenetic position of the Pterosauria within the Archosauromorpha

In recent years the hypothesis that pterosaurs were the major sister-group of dinosaurs and a closely-linked hypothesis that pterosaurs evolved flight from the ground up have gained general acceptance. A cladistic analysis of the Archosauromorpha using characters presented by previous workers results in a single most parsimonious tree with the Pterosauria as the major sister-group of the Dinosauria. However, that sister-group relationship is supported only by a suite of hindlimb characters that are correlated with bipedal digitigrade locomotion in dinosaurs. In pterosaurs the characters have been interpreted as correlates of bipedal cursorial locomotion, arboreal leaping, or involvement of the hindlimb in the wing. The homology of those characters in dinosaurs and pterosaurs cannot be supported. Reanalysis of the data after exclusion of those hindlimb characters results in most parsimonious trees with the Pterosauria as the sister-group of the Erythrosuchidae + Proterochampsidae + Euparkeria + Archosauria, in that order. This sister-group relationship is supported by a diverse assemblage of functionally independent skeletal characters from all regions of the skeleton. The results of the analysis cast doubt on the hypothesis that pterosaurs evolved flight from the ground up.     

Relationship between lordosis and the position of the centre of reaction of the spinal disc

Whenever we stand upright in apparent static equilibrium, we are, in fact, continuously making minor adjustments in order to maintain our balance. For each intervertebral joint, a point must exist at which all moments applied to the joint are continually and dynamically balanced. This point, known as the centre of reaction, is a mathematical invention necessary to perform analyses of spinal motion, but which need not be associated with any real anatomical structure.As the spine flexes and extends, this centre is expected to move; where it moves and the rationale for its motion is worthy of enquiry. In this paper, we propose that the centre of reaction remains confined to the nucleus of the disc, but only if one simple but crucial assumption is made; that the motion of the spine and control of its musculature maintain a minimum and equal stress at each intervertebral joint. This is a simple hypothesis which imposes a very specific relationship between lordosis and the centre of reaction. We investigate this relationship and its consequences on the teaching of lifting.The impossibility of designing experiments adequately to verify this hypothesis prevents in vivo verification, and, therefore, the model's verification must be made through the inferred consequences. For example, the capability of correctly predicting physiological responses of the musculoskeletal system is an indication of the validity of a model; however, this is not universally accepted. In this particular case, additional experimental data are available in the form of the locus of the centre of rotation of a vertebra vis-à-vis its lower neighbour as the spine flexes and extends.It is instructive to compare the predicted locus of the centre of reaction to experimentally determined locus of the centre of rotation; more than just coincidental similarities are found.     

Automatic calculation of epileptogenic focus location within the brain

The authors propose a hypothesis about the mathematical relationship between the position and intensity of epileptogenic discharge and the potential recorded from an electrocorticographic electrode. A computer program is used to solve the equation and to determine a small area of maximal probability for the focus to be found.     

Seabird species assemblages reflect hydrographic and biogeographic zones within Drake Passage

Polar Biology - Drake Passage, extending from the southern tip of South America to the northern Antarctic Peninsula, is a dynamic oceanographic region with well-defined habitats delineated by the...     

Spatial interactions within modular organisms: genetic heterogeneity and organism fitness

Modular organisms are composed of iterated units of construction that vary in their spatial arrangement. This variation is expected to affect the fitness of modular organisms due to interactions among neighboring modules and the potential for such organisms to be genetically heterogeneous. We devise a spatially explicit model to investigate how spatial interactions among neighboring modules affect organism fitness. We show that fitness is strongly dependent on the spatial arrangement of modules in both genetically homogeneous and heterogeneous organisms, and that the magnitude of the variation is dependent on the strength of interactions among modules. Organism fitness is more variable with interactions among modules that are symmetrical (each affects each other in the same directions) than with asymmetrical interactions (neighbors affect each other in different directions). We conclude by discussing potential extension of the present framework to a general dynamic model of spatially structured organism development.     

Membrane lateral diffusion and capture of CFTR within transient confinement zones

The cystic fibrosis transmembrane conductance regulator (CFTR) channel interacts with scaffolding and other proteins that are expected to restrict its lateral movement, yet previous studies have reported predominantly free diffusion. We examined the lateral mobility of CFTR channels on live baby hamster kidney cells using three complementary methods. Channels bearing an extracellular biotinylation target sequence were labeled with streptavidin conjugated with fluorescent dyes (Alexa Fluor 488 or 568) or quantum dots (qDot605). Fluorescence recovery after photobleaching and image correlation spectroscopy of the dye-labeled channels revealed a significant immobile population ( approximately 50%), which was confirmed by direct single particle tracking (SPT) of qDot605-labeled CFTR. Adding 10 histidine residues at the C-terminus of CFTR to mask the postsynaptic density 95, Discs large, ZO-1 (PDZ) binding motif abolished its association with EBP50/NHERF1, reduced the immobile fraction, and increased mobility. Other interactions that are not normally detected on this timescale became apparent when binding of PDZ domain proteins was disrupted. SPT revealed that CFTR(His-10) channels diffuse randomly, become immobilized for periods lasting up to 1 min, and in some instances are recaptured at the same location. The impact of transient confinement on the measured diffusion using the three fluorescence techniques were assessed using computer simulations of the biological experiments. Finally, the impact of endosomal CFTR on mobility measurements was assessed by fluorescence correlation spectroscopy. These results reveal unexpected features of CFTR dynamics which may influence its ion channel activity.     

Taxonomic position of the family Porcellanasteridae within the class Asteroidea

The phylogenetic relationships and taxonomic position of sea stars of the family Porcellanasteridae have been a subject of debate for over a hundred years. In this paper, the methods of molecular phylogenetic analysis were used to solve these issues. The nucleotide sequences of fragments of the mitochondrial gene of subunit 1 of cytochrome oxidase (COI) and those of the 16S rRNA gene were obtained for 9 and 6 species of porcellanasterids for the first time, respectively. The phylogenetic trees including these sequences indicate the nearest relationships of the family Porcellanasteridae with the families Ctenodiscidae and Goniopectinidae, thereby supporting the validity of the allocation of these three families in the suborder Cribellina.